[pkg-java] r15138 - in trunk/jalview/debian: . manpages wrappers
Vincent Fourmond
fourmond at alioth.debian.org
Thu Sep 29 23:07:55 UTC 2011
Author: fourmond
Date: 2011-09-29 23:07:55 +0000 (Thu, 29 Sep 2011)
New Revision: 15138
Added:
trunk/jalview/debian/jalview.manpages
trunk/jalview/debian/jalview.menu
trunk/jalview/debian/manpages/
trunk/jalview/debian/manpages/jalview.1
Removed:
trunk/jalview/debian/README.Debian
trunk/jalview/debian/menu.ex
Modified:
trunk/jalview/debian/changelog
trunk/jalview/debian/control
trunk/jalview/debian/copyright
trunk/jalview/debian/rules
trunk/jalview/debian/wrappers/jalview
Log:
[jalview] Make the package presentable -- and almost ready for upload !
Deleted: trunk/jalview/debian/README.Debian
===================================================================
--- trunk/jalview/debian/README.Debian 2011-09-29 21:31:49 UTC (rev 15137)
+++ trunk/jalview/debian/README.Debian 2011-09-29 23:07:55 UTC (rev 15138)
@@ -1,6 +0,0 @@
-jalview for Debian
-------------------
-
-<possible notes regarding this package - if none, delete this file>
-
- -- Vincent Fourmond <fourmond at debian.org> Thu, 15 Jan 2009 23:12:16 +0100
Modified: trunk/jalview/debian/changelog
===================================================================
--- trunk/jalview/debian/changelog 2011-09-29 21:31:49 UTC (rev 15137)
+++ trunk/jalview/debian/changelog 2011-09-29 23:07:55 UTC (rev 15138)
@@ -1,8 +1,9 @@
-jalview (2.6.1.dfsg-1) unstable; urgency=low
+jalview (2.6.1.dfsg~almost-1) unstable; urgency=low
* Initial release (Closes: #507436)
* Adding a debian/new-upstream script to repackage the original
tarball, getting rid of the bundled JAR file (I love JAR files)
+ (well, almost, which is why this goes in non-free for now)
* Using dh 7 and javahelper
* Using jh_build for building
Modified: trunk/jalview/debian/control
===================================================================
--- trunk/jalview/debian/control 2011-09-29 21:31:49 UTC (rev 15137)
+++ trunk/jalview/debian/control 2011-09-29 23:07:55 UTC (rev 15138)
@@ -1,5 +1,5 @@
Source: jalview
-Section: science
+Section: non-free/science
Priority: optional
Maintainer: Vincent Fourmond <fourmond at debian.org>
Build-Depends: cdbs, debhelper (>= 7), default-jdk,
@@ -27,5 +27,5 @@
alignement produced by programs implementing alignment algorithms
such as clustalw, kalign and t-coffee.
.
- It has lots of features, and can be considered a decent BioEdit
- replacement for Debian systems.
+ It has lots of features, and will compare advantageously to BioEdit,
+ while being free as in free speech !
Modified: trunk/jalview/debian/copyright
===================================================================
--- trunk/jalview/debian/copyright 2011-09-29 21:31:49 UTC (rev 15137)
+++ trunk/jalview/debian/copyright 2011-09-29 23:07:55 UTC (rev 15138)
@@ -1,52 +1,66 @@
-This package was debianized by:
+Format: http://anonscm.debian.org/viewvc/dep/web/deps/dep5.mdwn?revision=174
+Upstream-Name: freecol
+Upstream-Contact: jalview-discuss at jalview.org
+Source:
+ The original tarball was made downloading the jalview-*.tar.gz
+ tarball on http://www.jalview.org/versions.html, and stripping most
+ of the binary-only jars excepted lib/vamsas-client.jar.
+ .
+ For more details, see the debian/new-upstream script that does precisely
+ this.
+Disclaimer:
+ The tarball contains a sourceless binary jar,
+ lib/vamsas-client.jar. Though the distribution and use of this file
+ is allowed by its copyright holders, the absence of source prevents
+ it from being integrated into Debian main.
- Vincent Fourmond <fourmond at debian.org> on Thu, 15 Jan 2009 23:12:16 +0100
+Files: *
+Copyright: Copyright 2007-2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+License: GPL-3+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this package; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ .
+ On Debian systems, the complete text of the GNU General Public
+ License version 3 can be found in `/usr/share/common-licenses/GPL-3'.
-It was downloaded from:
- <url://example.com>
+Files: debian/*
+Copyright: Copyright (C) 2009-2011 Vincent Fourmond <fourmond at debian.org>
+License: GPL-3+
+ (see above)
-Upstream Author(s):
+Files: lib/vamsas-client.jar
+Copyright:
+License: ...
- <put author's name and email here>
- <likewise for another author>
-
-Copyright:
-
- <Copyright (C) YYYY Firtname Lastname>
- <likewise for another author>
-
-License:
-
-### SELECT: ###
- This package is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2 of the License, or
- (at your option) any later version.
-### OR ###
- This package is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License version 2 as
- published by the Free Software Foundation.
-##########
-
- This package is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this package; if not, write to the Free Software
- Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-
-On Debian systems, the complete text of the GNU General
-Public License can be found in `/usr/share/common-licenses/GPL'.
-
-The Debian packaging is:
-
- Copyright C) 2009, Vincent Fourmond <fourmond at debian.org>
-
-and is licensed under the GPL, see above.
-
-
-# Please also look if there are files or directories which have a
-# different copyright/license attached and list them here.
+Files: src/com/stevesoft/pat/*
+Copyright: Copyright 2001, Steven R. Brandt
+License: LGPL3+
+ This package is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public License
+ as published by the Free Software Foundation; either version 3 of
+ the License, or (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+ .
+ You should have received a copy of the GNU Lesser General Public
+ License along with this package; if not, write to the Free
+ Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA
+ 02110-1301 USA
+ .
+ On Debian systems, the complete text of the GNU Lesser Public
+ License version 3 can be found in `/usr/share/common-licenses/LGPL-3'.
Added: trunk/jalview/debian/jalview.manpages
===================================================================
--- trunk/jalview/debian/jalview.manpages (rev 0)
+++ trunk/jalview/debian/jalview.manpages 2011-09-29 23:07:55 UTC (rev 15138)
@@ -0,0 +1 @@
+debian/manpages/jalview.1
\ No newline at end of file
Added: trunk/jalview/debian/jalview.menu
===================================================================
--- trunk/jalview/debian/jalview.menu (rev 0)
+++ trunk/jalview/debian/jalview.menu 2011-09-29 23:07:55 UTC (rev 15138)
@@ -0,0 +1,2 @@
+?package(jalview):needs="X11" section="Applications/Science/Biology"\
+ title="Jalview" command="/usr/bin/jalview"
Added: trunk/jalview/debian/manpages/jalview.1
===================================================================
--- trunk/jalview/debian/manpages/jalview.1 (rev 0)
+++ trunk/jalview/debian/manpages/jalview.1 2011-09-29 23:07:55 UTC (rev 15138)
@@ -0,0 +1,34 @@
+.\" Hey, EMACS: -*- nroff -*-
+.\" First parameter, NAME, should be all caps
+.\" Copyright 2011 by Vincent Fourmond
+.\" Can be modified and distributed under the terms of the GNU General
+.\" public license, version 3 or any later version at your option.
+.TH JALVIEW 1 "26-01-2009"
+.SH NAME
+jalview \- Sequence alignement viewer
+.SH SYNOPSIS
+.B jalview
+
+.SH DESCRIPTION
+
+.B jalview
+provides facilities for viewing/editing and otherwise manipulating
+sequence alignments (DNA, amino acids).
+
+
+.SH JAVA-WRAPPERS NOTE
+
+This program is a shell script wrapper based on
+.BR java-wrappers (7).
+You therefore benefit from several features; please see the
+.BR java-wrappers (7)
+manual page for more information about them.
+
+
+.SH SEE ALSO
+
+.B http://www.jalview.org
+
+.SH AUTHOR
+This manual page was written by Vincent Fourmond <fourmond at debian.org>
+from the Debian project, but may be used by others.
Deleted: trunk/jalview/debian/menu.ex
===================================================================
--- trunk/jalview/debian/menu.ex 2011-09-29 21:31:49 UTC (rev 15137)
+++ trunk/jalview/debian/menu.ex 2011-09-29 23:07:55 UTC (rev 15138)
@@ -1,2 +0,0 @@
-?package(jalview):needs="X11|text|vc|wm" section="Applications/see-menu-manual"\
- title="jalview" command="/usr/bin/jalview"
Modified: trunk/jalview/debian/rules
===================================================================
--- trunk/jalview/debian/rules 2011-09-29 21:31:49 UTC (rev 15137)
+++ trunk/jalview/debian/rules 2011-09-29 23:07:55 UTC (rev 15138)
@@ -22,5 +22,9 @@
axis jh lib/vamsas-client.jar /usr/share/jmol-applet/JmolApplet.jar
-ANT_OPTS := -Dbuild.sysclasspath=last -DPACKAGE_VERSION=$(VERSION)
+ANT_OPTS := -Dbuild.sysclasspath=last \
+ -DJALVIW_VERSION=$(VERSION)
+FINAL_CLASSPATH = $(subst lib/vamsas-client.jar, /usr/share/jalview/vamsas-client.jar, $(DEB_CLASSPATH))
+
+JH_CLASSPATH_ARGS := -c"$(shell echo $(FINAL_CLASSPATH) | sed 's/:/ /g')" debian/jalview/usr/share/java/jalview.jar
Modified: trunk/jalview/debian/wrappers/jalview
===================================================================
--- trunk/jalview/debian/wrappers/jalview 2011-09-29 21:31:49 UTC (rev 15137)
+++ trunk/jalview/debian/wrappers/jalview 2011-09-29 23:07:55 UTC (rev 15138)
@@ -6,10 +6,6 @@
# We need openjdk or sun6
find_java_runtime openjdk sun6
-find_jars castor-xml commons-logging log4j-1.2 \
- castor-core Jmol min-jaba-client axis-jaxrpc \
- axis jh /usr/share/jalview/vamsas-client.jar \
- /usr/share/jmol-applet/JmolApplet.jar \
- jalview
+find_jar_classpath jalview
run_java jalview.bin.Jalview "$@"
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